def get_closest_reverse_read(self, read):
closest_reverse_read = None
if read.query_name.split('_')[-1] == '1':
positions = sorted(list(self.reverse_reads_mate2_positions[read.reference_name].keys()))
closest_pos = misc.takeClosestLarger(positions, read.reference_start)
if closest_pos is not None:
closest_reverse_read = self.reverse_reads_mate2_positions[read.reference_name][closest_pos]
else:
positions = sorted(list(self.reverse_reads_mate1_positions[read.reference_name].keys()))
closest_pos = misc.takeClosestLarger(positions, read.reference_start)
if closest_pos is not None:
closest_reverse_read = self.reverse_reads_mate1_positions[read.reference_name][closest_pos]
return closest_reverse_read
def has_nearby_5p_mate(self, pos, positions):
closest_5p = misc.takeClosestLarger(positions, pos)
if closest_5p is None:
return False
if closest_5p - pos <= self.min_distance_to_mate:
return True
else:
return False